diff --git a/pkgs/build-support/build-bazel-package/default.nix b/pkgs/build-support/build-bazel-package/default.nix
index 1131f73a1836..becda0c2867b 100644
--- a/pkgs/build-support/build-bazel-package/default.nix
+++ b/pkgs/build-support/build-bazel-package/default.nix
@@ -30,6 +30,7 @@ args@{
   # [1]: https://github.com/bazelbuild/rules_cc
 , removeRulesCC ? true
 , removeLocalConfigCc ? true
+, removeLocalConfigSh ? true
 , removeLocal ? true
 
   # Use build --nobuild instead of fetch. This allows fetching the dependencies
@@ -154,10 +155,16 @@ stdenv.mkDerivation (fBuildAttrs // {
       # Remove all built in external workspaces, Bazel will recreate them when building
       rm -rf $bazelOut/external/{bazel_tools,\@bazel_tools.marker}
       ${lib.optionalString removeRulesCC "rm -rf $bazelOut/external/{rules_cc,\\@rules_cc.marker}"}
+
       rm -rf $bazelOut/external/{embedded_jdk,\@embedded_jdk.marker}
       ${lib.optionalString removeLocalConfigCc "rm -rf $bazelOut/external/{local_config_cc,\\@local_config_cc.marker}"}
       ${lib.optionalString removeLocal "rm -rf $bazelOut/external/{local_*,\\@local_*.marker}"}
 
+      # For bazel version >= 6 with bzlmod.
+      ${lib.optionalString removeLocalConfigCc "rm -rf $bazelOut/external/*[~+]{local_config_cc,local_config_cc.marker}"}
+      ${lib.optionalString removeLocalConfigSh "rm -rf $bazelOut/external/*[~+]{local_config_sh,local_config_sh.marker}"}
+      ${lib.optionalString removeLocal "rm -rf $bazelOut/external/*[~+]{local_jdk,local_jdk.marker}"}
+
       # Clear markers
       find $bazelOut/external -name '@*\.marker' -exec sh -c 'echo > {}' \;
 
diff --git a/pkgs/by-name/ba/bant/package.nix b/pkgs/by-name/ba/bant/package.nix
index daad4e7b0b2d..c91652b47cd1 100644
--- a/pkgs/by-name/ba/bant/package.nix
+++ b/pkgs/by-name/ba/bant/package.nix
@@ -40,8 +40,8 @@ buildBazelPackage rec {
   fetchAttrs = {
     hash =
       {
-        aarch64-linux = "sha256-8pLgn67kwVNdqhUXYsdi7OsArCZZmW55UPzUBlIyBbk=";
-        x86_64-linux = "sha256-dUNdvSJA3SlIIRWmhaq3Hu0+84mBBhxbU/eBDXIv/iI=";
+        aarch64-linux = "sha256-M6LMaqPli71YvJS/4iwvowCyVaf+qe8WSICR3CgdU34=";
+        x86_64-linux = "sha256-iBxAzbSriYkkgDDkSjSSSVeWGBygxKAfruh8T5drUFw=";
       }
       .${system} or (throw "No hash for system: ${system}");
   };
diff --git a/pkgs/by-name/pe/perf_data_converter/package.nix b/pkgs/by-name/pe/perf_data_converter/package.nix
index 9c15422977d9..439536cc6cae 100644
--- a/pkgs/by-name/pe/perf_data_converter/package.nix
+++ b/pkgs/by-name/pe/perf_data_converter/package.nix
@@ -38,8 +38,8 @@ buildBazelPackage rec {
   fetchAttrs = {
     hash =
       {
-        aarch64-linux = "sha256-F4fYZfdCmDzJRR+z1rCLsculP9y9B8H8WHNQbFZEv+s=";
-        x86_64-linux = "sha256-rjlquK0WcB7Te2uUKKVOrL7+6PtcWQImUWTVafIsbHY=";
+        aarch64-linux = "sha256-Ksae4VC2FbkW79N5EGn/rTdj+GFKQsZCdi4LPfnzV7Y=";
+        x86_64-linux = "sha256-TYeS1bax7sA0hJLXqtE8Q5FLnIylcWPZynVE2LhvZKc=";
       }
       .${system} or (throw "No hash for system: ${system}");
   };